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- PDB-8aj5: X-ray structure of lysozyme obtained upon reaction with [VIVO(mal... -

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Basic information

Entry
Database: PDB / ID: 8aj5
TitleX-ray structure of lysozyme obtained upon reaction with [VIVO(malt)2] (Structure B)
ComponentsLysozyme
KeywordsHYDROLASE / metallodrug / vanadium / oxidovanadium / covalent binding / non-covalent binding / protein-metal interaction
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / NITRATE ION / VANADATE ION / bis(oxidanyl)vanadium / oxovanadium(2+) / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsPaolillo, M. / Merlino, A. / Ferraro, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Inorg.Chem. / Year: 2022
Title: Multiple and Variable Binding of Pharmacologically Active Bis(maltolato)oxidovanadium(IV) to Lysozyme.
Authors: Ferraro, G. / Paolillo, M. / Sciortino, G. / Garribba, E. / Merlino, A.
History
DepositionJul 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,46517
Polymers14,3311
Non-polymers1,13416
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.230, 78.230, 37.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11AAA-206-

VVB

21AAA-206-

VVB

31AAA-330-

HOH

41AAA-352-

HOH

51AAA-385-

HOH

61AAA-415-

HOH

71AAA-430-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Lysozyme


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698

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Non-polymers , 7 types, 148 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-VVO / oxovanadium(2+)


Mass: 66.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: OV / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-VVB / bis(oxidanyl)vanadium


Mass: 84.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2V / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20% ethylene glycol 0.1 M sodium acetate pH 4.0 0.6 M sodium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.31→55.32 Å / Num. obs: 28122 / % possible obs: 98.9 % / Redundancy: 20 % / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Net I/σ(I): 14.3
Reflection shellResolution: 1.31→1.33 Å / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 25.8 / Num. unique obs: 28122 / CC1/2: 0.755 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193l

193l


Resolution: 1.31→55.317 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.926 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1976 1403 4.999 %
Rwork0.1676 26662 -
all0.169 --
obs-28065 98.779 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.925 Å2
Baniso -1Baniso -2Baniso -3
1-0.037 Å2-0 Å2-0 Å2
2--0.037 Å2-0 Å2
3----0.073 Å2
Refinement stepCycle: LAST / Resolution: 1.31→55.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 61 132 1194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131158
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141032
X-RAY DIFFRACTIONr_angle_refined_deg1.8391.6251560
X-RAY DIFFRACTIONr_angle_other_deg1.581.5992351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.26619.86172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83115187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7451515
X-RAY DIFFRACTIONr_chiral_restr0.0930.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021400
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02318
X-RAY DIFFRACTIONr_nbd_refined0.2760.2298
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.2950
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2543
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2453
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0840.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.213
X-RAY DIFFRACTIONr_nbd_other0.270.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.228
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1190.21
X-RAY DIFFRACTIONr_mcbond_it1.671.61556
X-RAY DIFFRACTIONr_mcbond_other1.6161.6553
X-RAY DIFFRACTIONr_mcangle_it2.3892.415703
X-RAY DIFFRACTIONr_mcangle_other2.392.419704
X-RAY DIFFRACTIONr_scbond_it2.9052.097602
X-RAY DIFFRACTIONr_scbond_other2.7872.017579
X-RAY DIFFRACTIONr_scangle_it4.2642.942857
X-RAY DIFFRACTIONr_scangle_other4.1312.857834
X-RAY DIFFRACTIONr_lrange_it6.64921.3911428
X-RAY DIFFRACTIONr_lrange_other6.64821.4171429
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.31-1.3440.2661090.26118730.26220620.8880.87396.12030.248
1.344-1.3810.2381090.24518380.24420110.9030.89796.81750.222
1.381-1.4210.232890.22718660.22719770.9080.9298.88720.2
1.421-1.4650.239850.21817600.21918730.9220.92698.50510.191
1.465-1.5130.212970.19317090.19418450.9410.93797.88620.171
1.513-1.5660.204740.19516910.19617970.9410.93998.21930.171
1.566-1.6250.207790.18216290.18417320.9390.95198.61430.161
1.625-1.6910.231800.1715700.17216610.9330.95699.33780.152
1.691-1.7660.203850.16515050.16715970.9430.95999.56170.153
1.766-1.8520.173830.16114520.16215470.9590.96399.22430.152
1.852-1.9520.197750.15613670.15814530.9580.96799.24290.153
1.952-2.070.227680.1513210.15413990.9480.96799.28520.15
2.07-2.2130.21600.14612480.14913110.9550.9799.77120.155
2.213-2.390.145640.1411500.14112160.9750.97399.83550.152
2.39-2.6180.2560.14910820.15111380.9580.9721000.168
2.618-2.9260.183500.1489920.1510420.9650.971000.175
2.926-3.3770.191500.1558770.1579270.9610.9691000.191
3.377-4.1320.165420.157570.1517990.9710.9731000.193
4.132-5.8280.185310.1555940.1576250.9770.9791000.214
5.828-55.3170.289170.2713730.2723920.9550.92299.48980.374

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